6.1 Supported Formats

Table 6-1 contains the formats supported by Readseq. ID is a number that can be used for this format (name is prefered). Alternate Names are separated by using the | character. You can use any of these names to specify a format. R and W indicate if Readseq can read and write this format. I means the format is interleaved. F indicates that sequence record documentation and features are parsed. S indicates that the format contains sequence data. Content-type is the magic string sent for that format through a CGI web server. The suffix is the standard file suffix used for that format.

Table 6-1. Supported formats for Readseq

ID

Name

R

W

I

F

S

Content-type

Suffix

1

GenBank|gb

T

T

F

T

T

biosequence/genbank

.gb

2

EMBL|em

T

T

F

T

T

biosequence/embl

.embl

3

Pearson|Fasta|fa

T

T

F

F

T

biosequence/fasta

.fasta

4

GCG

T

T

F

F

T

biosequence/gcg

.gcg

5

MSF

T

T

T

F

T

biosequence/msf

.msf

6

Clustal

T

T

T

F

T

biosequence/clustal

.aln

7

NBRF

T

T

F

F

T

biosequence/nbrf

.nbrf

8

PIR|CODATA

T

T

F

F

T

biosequence/codata

.pir

9

ACEDB

T

T

F

F

T

biosequence/acedb

.ace

10

Phylip3.2

T

T

T

F

T

biosequence/phylip2

.phylip2

11

Phylip|Phylip4

T

T

T

F

T

biosequence/phylip

.phylip

12

Plain|Raw

T

T

F

F

T

biosequence/plain

.seq

13

PAUP|NEXUS

T

T

T

F

T

biosequence/nexus

.nexus

14

XML

T

T

F

T

T

biosequence/xml

.xml

15

FlatFeat|FFF

T

T

F

T

F

biosequence/fff

.fff

16

GFF

T

T

F

T

F

biosequence/gff

.gff

17

BLAST

T

F

T

F

T

biosequence/blast

.blast

18

Pretty

F

T

T

F

T

biosequence/pretty

.pretty

19

SCF

T

F

F

F

T

biosequence/scf

.scf

20

DNAStrider

T

T

F

F

T

biosequence/strider

.strider

21

IG|Stanford

T

T

F

F

T

biosequence/ig

.ig

22

Fitch

F

F

F

F

T

biosequence/fitch

.fitch

23

ASN.1

F

F

F

F

T

biosequence/asn1

.asn



Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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